I'm not sure how to see the value #s for the hospital zone, but you got me thinking, it would be much better to have the all the medical guilds in the hospital's common area, rather than in the basement below the hospital. I first added the surgeon's guild, without deleting it from the basement area, and the value of that guild increased. Erasing the guild zone on the lower level reduced that guild's value (as one should expect). Erasing the overlapping guilds however, 1 at a time, did not result in the remaining guilds increasing in value at all. Down to the last guild that was moved, it's value remained the same the whole time. I have not found a way to create guild overlaps that reduces their value at all.
Erasing the zone either in 1 click with the button, or with the eraser did not erase the guild zone on the floor above. I was relieved to find this is the case.
For guild halls, in order to create multi-z leveled halls, you have to make a new zone on each z level first, then assign it to the zone. Each additional chunk assigned in that way does increase the total guild hall value.
I would like to see if I can wall in the artifact pedestal in the basement, reduce all those zones to that 1 tile, and see if everyone moves their gathering to the common area above, while keeping the artifacts safely secured boosting their guild values equally. But the trade caravan arrived for the first time in a couple years, and there is a lot of designating to do...
Edit: As BlueTrillium has found above, I also confirmed that adding a guild hall over the pedestal in the "royal mausoleum" reduced its value to a "grave".
If I'm understanding it right, it seems that the top level zone creations (bedrooms, offices, dining halls, and tombs at least) go to zero value when overlapped with anything. But the locations assigned to those zones overlap without penalty. I was under the impression that the values were reduced linearly in proportion to the number of zones present and not all or nothing. But all or nothing is indeed simpler.
To keep everyone dining together, I'm adding some pedestal-view dining sections to the main hall for the various nobles. Still very much a work in progress
(https://i.imgur.com/ojwbRUK.jpg)